Re: [AMBER] Time numbering problem with constant-pH simulations

From: Daniel Roe <>
Date: Tue, 18 Aug 2020 09:02:47 -0400


Could you send me (off-list) the CPIN file in question? Also, I'm sure
that the CPOUT files are probably too large, but could you try to send
even a portion of them? In addition, maybe send the topology and
restart file as well. Any additional information (AmberTools/cpptraj
version etc) will be helpful. Thanks,


On Sat, Aug 15, 2020 at 10:32 AM Jonee Lillard <> wrote:
> Dear Sir or Madam:
> I have been running three rather long constant-pH simulations of a
> 164-residue protein. The simulations have been going fine, but their output
> has been mostly unanalyzable. Attached is the input file I have been using
> for the simulations.
> The first four production runs of each simulation have worked fine in the
> command-line cphstats functionality specified in Tutorial 18. However, the
> fifth and subsequent runs produce the following error:
> $cphstats -i dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout -o
> md5.calcpka.dat
> *Did not recognize the format of cpout dio1.mono.cpH.md5.cpout.Error: Cpout
> file dio1.mono.cpH.md5.cpout is invalid! Skipping.Error: Number of Cpout
> files 0 does not equal number specified: 1*
> Attempting to run them in CPPTRAJ does not work and yields the following
> error, though this seems to be dependent on the format of the .cpin files
> rather than the .cpout files.
> >readdata dio1.mono.cpH.md5.cpout cpin dio1.mono.cpH.md4.cpin
> [readdata dio1.mono.cpH.md5.cpout cpin dio1.mono.cpH.md4.cpin]
> Reading 'dio1.mono.cpH.md5.cpout' as Amber CPOUT with name
> 'dio1.mono.cpH.md5.cpout'
> System: Unknown
> Error: Number of states in CPIN (50) != TRESCNT in CPIN (21)
> Error: Could not read CPIN file 'dio1.mono.cpH.md4.cpin'
> Error: reading datafile dio1.mono.cpH.md5.cpout
> Error: Could not read data file 'dio1.mono.cpH.md5.cpout'.
> Attempting to use cphstats in CPPTRAJ results in this error.
> > cphstats -dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout name
> md5.calcpka.dat
> [cphstats -dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout name
> md5.calcpka.dat]
> Warning: '-dio1.mono.cpH.md4.cpin' selects no data sets.
> Warning: 'dio1.mono.cpH.md5.cpout' selects no data sets.
> Error: No pH data sets.
> Error: Could not setup analysis [cphstats]
> I have also noticed that the numbering of the time values in the fifth and
> subsequent .cpout files runs out of characters in the file template and has
> asterisks instead. Could this be responsible for the failure of
> recognition, and if so, how can it be fixed or circumvented, whether
> through the command line or CPPTRAJ?
> -- Jonee
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Received on Tue Aug 18 2020 - 06:30:04 PDT
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